Table I. Interaction lists and confidence.
(A) Interacting proteins for FLW bait with FlyMine validation. n = number of times observed, cs = confidence score, PP = Protein Probability score (from MASCOT), d = putative direct interaction, i = indirect interaction, F_1/2 = FLAG experiment 1 or 2, S = Strep, Y2H = yeast 2-hybrid, FP = fragment pooling approach, PS = phenotypic suppression, PE = phenotypic enhancement, PD = pulldown, AC = Affinity Capture, CoIP = anti-tag coimmunoprecipitation. Confidence scores derived from Supplementary Fig. S3. Upper row in bold identifies the bait, bold grey highlighted are direct interactions or proteins validated by two independent methods and grey highlighted are those validated by one method. Italicised are potential contaminants. *plus ID codes 12134149, 12750335, 14605208, 15575970, 15710747, 17007873, 9230081.
| Uniprot ID | Gene name | Description | n | cs | PP mean | F1 | F2 | S1 | S2 | Experimental evidence | d/i | PubMed ID |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q8T0U6 | flw | Serine/threonine protein phosphatase | 4 | 1.00 | 601.8 | 1 | 1 | 1 | 1 | |||
| Q9VUX6 | Mbs | CG32156-PA | 4 | 1.00 | 337.5 | 1 | 1 | 1 | 1 | Y2H-FP, FB | d | 15710747 |
| Q9VBD6 | CG5471 | CG5471-PA | 3 | 0.80 | 97.3 | 1 | 0 | 1 | 1 | Y2H | i | 14605208 |
| Q8IM86 | unc-13 | CG2999-PB | 3 | 0.80 | 76.0 | 0 | 1 | 1 | 1 | Y2H | i | 14605208 |
| P28668 | Aats-glupro | Bifunctional aminoacyl-tRNA synthetase | 3 | 0.80 | 57.7 | 0 | 1 | 1 | 1 | |||
| Q8SXP0 | CG8709 | GH19076p | 3 | 0.80 | 46.7 | 0 | 1 | 1 | 1 | Y2H | i | 14605208 |
| Q94883 | Dref | CG5838-PA | 3 | 0.80 | 35.7 | 0 | 1 | 1 | 1 | |||
| P05661–19 | Mhc | Myosin Heavy Chain-PF | 2 | 0.50 | 244.0 | 1 | 0 | 0 | 1 | Y2H-FP | i | 15710747 |
| P12982 | Pp1–87B | Serine/threonine-protein phosphatase α-2 isoform | 2 | 0.50 | 127.5 | 1 | 0 | 1 | 0 | CoIP, PE, PS, Y2H, Y2H-FP | d | 11514446, 11729158* |
| Q9VMT8 | CG33715 | Muscle specific protein | 2 | 0.50 | 124.0 | 0 | 1 | 0 | 1 | |||
| Q9VLT5 | poe | Protein purity of essence | 2 | 0.50 | 105.0 | 0 | 1 | 0 | 1 | |||
| Q9VB44 | CG3339 | CG3339-PA | 2 | 0.50 | 102.5 | 0 | 1 | 0 | 1 | |||
| Q27331 | Vha68–2 | Vacuolar ATP synthase catalytic subunit A isoform 2 | 2 | 0.50 | 97.0 | 0 | 1 | 0 | 1 | |||
| Q9VBE2 | CG5468 | CG5468-PA | 2 | 0.50 | 90.5 | 0 | 1 | 1 | 0 | Y2H | i | 14605208 |
| Q9VNE0 | CG2926 | CG2926-PA | 2 | 0.50 | 80.5 | 0 | 1 | 0 | 1 | Y2H-FP | i | 15710747 |
| Q9W2Z4 | CG2990 | CG2990-PA | 2 | 0.50 | 77.5 | 0 | 1 | 0 | 1 | |||
| Q9W2Z3 | CG2989 | CG2989-PA | 2 | 0.50 | 76.0 | 0 | 1 | 0 | 1 | |||
| Q9W053 | zormin | CG33484-PA | 2 | 0.50 | 72.5 | 0 | 1 | 0 | 1 | Y2H, Y2H-FP | i | 14605208, 15710747 |
| Q8I8U7 | Nipped-A | Transcription-associated protein 1 | 2 | 0.50 | 72.5 | 0 | 1 | 0 | 1 | Y2H FP, AC-western | i | 15710747, 12697829 |
| Q9VZQ3 | kst | CG12008-PA | 2 | 0.50 | 70.5 | 0 | 1 | 0 | 1 | Y2H, Y2H-FP | i | 14605208, 15710747 |
| (B) Summary of interacting proteins from the other selected baits and validation analysis using FlyMine. Lists of interacting proteins for the remaining proteins are in supplementary Tables S4a-f.[1]. *after removal of negative controls (W-), ¶ based on FlyMine and DroID, + after removal of single IDs. No's in parentheses indicate proteins found >10% of contaminants lists. | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Bait | No. of hits* |
Published Interactors¶ |
Validated Interactors+ |
||||||||
| Total | Score≥ 0.75 | Score>0.2-<0.75 | Score≤ 0.2 | Total (inc. genetic) | Affinity method | % | Direct (with bait) | Direct (all) | Orthologs (direct bait) | Indirect (with bait) | |
| FLW | 460 | 7(2) | 49(11) | 405 | 55 | 1 | 44 | 8 | 81 | 2 | 37 |
| SGG | 843 | 12(1) | 83(7) | 748 | 31 | 1 | 48 | 0 | 18 | 5 | 0 |
| RTNL1 | 166 | 1 | 3(1) | 162 | 10 | 0 | 50 | 0 | 1 | 0 | 7 |
| FAS2(A) | 209 | 1(1) | 4(1) | 204 | 16 | 2 | 64 | 1 | 30 | 0 | 9 |
| FAS2(B) | 583 | 11(7) | 46(13) | 526 | 16 | 2 | 69 | 1 | 124 | 0 | 19 |
| SEMA-1A | 129 | 3(3) | 26(10) | 100 | 7 | 0 | 56 | 0 | 12 | 0 | 6 |
| DP | 28 | 0 | 0 | 28(16) | 2 | 0 | 12 | 0 | 1 | 0 | 0 |
| PKA-R2 | 63 | 1 | 15 | 47 | 8 | 0 | 50 | 2 | 11 | 6 | 1 |
| fl(2)d | 29 | 0 | 5 | 24 | 20 | 3 | 68 | 2 | 2 | 0 | 2 |
| ATPsyn-β | 91 | 6 | 12 | 73 | 25 | 0 | 81 | 1 | 12 | 20 | 12 |
| CAM | 84 | 0 | 2 | 82 | 32 | 0 | 38 | 0 | 6 | 1 | 9 |
| GS2 | 78 | 1 | 18 | 59 | 1 | 0 | 71 | 0 | 15 | 12 | 1 |
| NOTCH | 315 | 0 | 6 | 309 | 183 | 1 | 64 | 3 | 54 | 7 | 63 |
| BEL | 43 | 0 | 2 | 41 | 0 | 0 | 57 | 0 | 6 | 15 | 0 |